Pool stats for all and low coverage

• Species is already checked during trimming step

• In “sample_sheet.tsv”" (input for alignment-nf), there may be multiple replicate libraries (“id”) for the same strain (“strain”). Here will output stats for all replicates combined.

• Output stats_strain_all.tsv contains stats for all strains, with all replicates combined.

• Output stats_strains_with_low_values.tsv contains strains with:

  • either (1) total raw reads < 10000, not enough to do anything;
  • or (2) reads mapping rate < 70%, which indicates wrong species, or lib quality issue.
  • or (3) average coverage across main chromosomes < 14x, which is not enough for variant calling.

• Output sample_sheet_for_seq_sheet.tsv is formatted to be put on to Google sequencing sheet, which contains a column of coverage.

## [1] "strains with too few reads (< 10000): "

plot to see cutoff for percent reads mapped and average coverage

If a strain had most reads mapped (> 90%, indicating correct species), and coverage is a bit low (between 10x ~ 15x), probably still worth keeping for variant calling.

Low coverage strains

## [1] "low reads input: 0 strains"

## [1] "low percent reads mapped: 0 strains"

## [1] "low average coverage: 14 strains"

## R version 3.6.0 (2019-04-26)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Red Hat Enterprise Linux Server 7.5 (Maipo)
## 
## Matrix products: default
## BLAS:   /hpc/software/R/3.6.0/lib64/R/lib/libRblas.so
## LAPACK: /hpc/software/R/3.6.0/lib64/R/lib/libRlapack.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] plotly_4.9.2    forcats_0.4.0   stringr_1.4.0   dplyr_0.8.4    
##  [5] purrr_0.3.3     readr_1.3.1     tidyr_1.0.2     tibble_2.1.3   
##  [9] ggplot2_3.2.1   tidyverse_1.3.0
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.6        lubridate_1.7.4   lattice_0.20-38   assertthat_0.2.1 
##  [5] digest_0.6.24     mime_0.9          R6_2.4.1          cellranger_1.1.0 
##  [9] backports_1.1.5   reprex_0.3.0      evaluate_0.14     httr_1.4.1       
## [13] pillar_1.4.3      rlang_0.4.4       lazyeval_0.2.2    readxl_1.3.1     
## [17] rstudioapi_0.11   data.table_1.12.8 DT_0.12           rmarkdown_2.1    
## [21] labeling_0.3      htmlwidgets_1.5.1 munsell_0.5.0     shiny_1.4.0      
## [25] broom_0.5.4       compiler_3.6.0    httpuv_1.5.2      modelr_0.1.5     
## [29] xfun_0.12         pkgconfig_2.0.3   htmltools_0.4.0   tidyselect_1.0.0 
## [33] fansi_0.4.1       viridisLite_0.3.0 crayon_1.3.4      dbplyr_1.4.2     
## [37] withr_2.1.2       later_1.0.0       grid_3.6.0        xtable_1.8-4     
## [41] nlme_3.1-139      jsonlite_1.6.1    gtable_0.3.0      lifecycle_0.1.0  
## [45] DBI_1.1.0         magrittr_1.5      scales_1.1.0      cli_2.0.1        
## [49] stringi_1.4.6     farver_2.0.3      fs_1.3.1          promises_1.1.0   
## [53] xml2_1.2.2        generics_0.0.2    vctrs_0.2.2       tools_3.6.0      
## [57] glue_1.3.1        hms_0.5.3         crosstalk_1.0.0   fastmap_1.0.1    
## [61] yaml_2.2.1        colorspace_1.4-1  rvest_0.3.5       knitr_1.28       
## [65] haven_2.2.0